OpenRaiser/Intern-Atlas huggingface dataset:
Maven-Hijack: Software Supply Chain Attack Exploiting Packaging Order
Venue: arXiv cs.CR 2025
Year: 2025

Java projects frequently rely on package managers such as Maven to manage complex webs of external dependencies. While these tools streamline development, they also introduce subtle risks to the software supply chain. In this paper, we present Maven-Hijack, a novel attack that exploits the order in which Maven packages dependencies and the way the Java Virtual Machine resolves classes at runtime. By injecting a malicious class with the same fully qualified name as a legitimate one into a dependency that is packaged earlier, an attacker can silently override core application behavior without modifying the main codebase or library names. We demonstrate the real-world feasibility of this attack by compromising the Corona-Warn-App, a widely used open-source COVID-19 contact tracing system, and gaining control over its database connection logic. We evaluate three mitigation strategies, such as sealed JARs, Java Modules, and the Maven Enforcer plugin. Our results show that, while Java Modules offer strong protection, the Maven Enforcer plugin with duplicate class detection provides the most practical and effective defense for current Java projects. These findings highlight the urgent need for improved safeguards in Java's build and dependency management processes to prevent stealthy supply chain attacks.
Foundation Models for the Digital Twin Creation of Cyber-Physical Systems
Venue: arXiv cs.SE 2025
Year: 2025

Foundation models are trained on a large amount of data to learn generic patterns. Consequently, these models can be used and fine-tuned for various purposes. Naturally, studying such models' use in the context of digital twins for cyber-physical systems (CPSs) is a relevant area of investigation. To this end, we provide perspectives on various aspects within the context of developing digital twins for CPSs, where foundation models can be used to increase the efficiency of creating digital twins, improve the effectiveness of the capabilities they provide, and used as specialized fine-tuned foundation models acting as digital twins themselves. We also discuss challenges in using foundation models in a more generic context. We use the case of an autonomous driving system as a representative CPS to give examples. Finally, we provide discussions and open research directions that we believe are valuable for the digital twin community.
Disturbance-based Discretization, Differentiable IDS Channel, and an IDS-Correcting Code for DNA-based Storage
Venue: arXiv cs.IT 2025
Year: 2025

With recent advancements in next-generation data storage, especially in biological molecule-based storage, insertion, deletion, and substitution (IDS) error-correcting codes have garnered increased attention. However, a universal method for designing tailored IDS-correcting codes across varying channel settings remains underexplored. We present an autoencoder-based approach, THEA-code, aimed at efficiently generating IDS-correcting codes for complex IDS channels. In the work, a disturbance-based discretization is proposed to discretize the features of the autoencoder, and a simulated differentiable IDS channel is developed as a differentiable alternative for IDS operations. These innovations facilitate the successful convergence of the autoencoder, producing channel-customized IDS-correcting codes that demonstrate commendable performance across complex IDS channels, particularly in realistic DNA-based storage channels.
Unexplainability of Artificial Intelligence Judgments in Kant's Perspective
Venue: arXiv cs.AI 2025
Year: 2025

Kant's Critique of Pure Reason, a major contribution to the history of epistemology, proposes a table of categories to elucidate the structure of the a priori principles underlying human judgment. Artificial intelligence (AI) technology, grounded in functionalism, claims to simulate or replicate human judgment. To evaluate this claim, it is necessary to examine whether AI judgments exhibit the essential characteristics of human judgment. This paper investigates the unexplainability of AI judgments through the lens of Kant's theory of judgment. Drawing on Kant's four logical forms-quantity, quality, relation, and modality-this study identifies what may be called AI's uncertainty, a condition in which different forms of judgment become entangled. In particular, with regard to modality, this study argues that the SoftMax function forcibly reframes AI judgments as possibility judgments. Furthermore, since complete definitions in natural language are impossible, words are, by their very nature, ultimately unexplainable; therefore, a fully complete functional implementation is theoretically unattainable.
To which reference class do you belong? Measuring racial fairness of reference classes with normative modeling
Venue: arXiv cs.LG 2025
Year: 2025

Reference classes in healthcare establish healthy norms, such as pediatric growth charts of height and weight, and are used to chart deviations from these norms which represent potential clinical risk. How the demographics of the reference class influence clinical interpretation of deviations is unknown. Using normative modeling, a method for building reference classes, we evaluate the fairness (racial bias) in reference models of structural brain images that are widely used in psychiatry and neurology. We test whether including race in the model creates fairer models. We predict self-reported race using the deviation scores from three different reference class normative models, to better understand bias in an integrated, multivariate sense. Across all of these tasks, we uncover racial disparities that are not easily addressed with existing data or commonly used modeling techniques. Our work suggests that deviations from the norm could be due to demographic mismatch with the reference class, and assigning clinical meaning to these deviations should be done with caution. Our approach also suggests that acquiring more representative samples is an urgent research priority.
Decomposing heterogeneous dynamical systems with graph neural networks
Venue: arXiv cs.LG 2025
Year: 2025

Natural physical, chemical, and biological dynamical systems are often complex, with heterogeneous components interacting in diverse ways. We show how simple graph neural networks can be designed to jointly learn the interaction rules and the latent heterogeneity from observable dynamics. The learned latent heterogeneity and dynamics can be used to virtually decompose the complex system which is necessary to infer and parameterize the underlying governing equations. We tested the approach with simulation experiments of interacting moving particles, vector fields, and signaling networks. While our current aim is to better understand and validate the approach with simulated data, we anticipate it to become a generally applicable tool to uncover the governing rules underlying complex dynamics observed in nature.
The Impact of LoRA Adapters on LLMs for Clinical Text Classification Under Computational and Data Constraints
Venue: arXiv cs.CL 2025
Year: 2025

Fine-tuning Large Language Models (LLMs) for clinical Natural Language Processing (NLP) poses significant challenges due to domain gap, limited data, and stringent hardware constraints. In this study, we evaluate four adapter techniques-Adapter, Lightweight, TinyAttention, and Gated Residual Network (GRN) - equivalent to Low-Rank Adaptation (LoRA), for clinical note classification under real-world, resource-constrained conditions. All experiments were conducted on a single NVIDIA Quadro P620 GPU (2 GB VRAM, 512 CUDA cores, 1.386 TFLOPS FP32), limiting batch sizes to <8 sequences and maximum sequence length to 256 tokens. Our clinical corpus comprises only 580 000 tokens, several orders of magnitude smaller than standard LLM pre-training datasets. We fine-tuned three biomedical pre-trained LLMs (CamemBERT-bio, AliBERT, DrBERT) and two lightweight Transformer models trained from scratch. Results show that 1) adapter structures provide no consistent gains when fine-tuning biomedical LLMs under these constraints, and 2) simpler Transformers, with minimal parameter counts and training times under six hours, outperform adapter-augmented LLMs, which required over 1000 GPU-hours. Among adapters, GRN achieved the best metrics (accuracy, precision, recall, F1 = 0.88). These findings demonstrate that, in low-resource clinical settings with limited data and compute, lightweight Transformers trained from scratch offer a more practical and efficient solution than large LLMs, while GRN remains a viable adapter choice when minimal adaptation is needed.
Accounting for plasticity: An extension of inelastic Constitutive Artificial Neural Networks
Venue: arXiv cs.LG 2025
Year: 2025

In this work, we extend the existing framework of inelastic constitutive artificial neural networks (iCANNs) by incorporating plasticity to increase their applicability to model more complex material behavior. The proposed approach ensures objectivity, material symmetry, and thermodynamic consistency, providing a robust basis for automatic model discovery of constitutive equations at finite strains. These are predicted by discovering formulations for the Helmholtz free energy and plastic potentials for the yield function and evolution equations in terms of feed-forward networks. Our framework captures both linear and nonlinear kinematic hardening behavior. Investigation of our model's prediction showed that the extended iCANNs successfully predict both linear and nonlinear kinematic hardening behavior based on experimental and artificially generated datasets, showcasing promising capabilities of this framework. Nonetheless, challenges remain in discovering more complex yield criteria with tension-compression asymmetry and addressing deviations in experimental data at larger strains. Despite these limitations, the proposed framework provides a promising basis for incorporating plasticity into iCANNs, offering a platform for advancing in the field of automated model discovery.
The Emerged Security and Privacy of LLM Agent: A Survey with Case Studies
Venue: arXiv cs.CR 2025
Year: 2025

Inspired by the rapid development of Large Language Models (LLMs), LLM agents have evolved to perform complex tasks. LLM agents are now extensively applied across various domains, handling vast amounts of data to interact with humans and execute tasks. The widespread applications of LLM agents demonstrate their significant commercial value; however, they also expose security and privacy vulnerabilities. At the current stage, comprehensive research on the security and privacy of LLM agents is highly needed. This survey aims to provide a comprehensive overview of the newly emerged privacy and security issues faced by LLM agents. We begin by introducing the fundamental knowledge of LLM agents, followed by a categorization and analysis of the threats. We then discuss the impacts of these threats on humans, environment, and other agents. Subsequently, we review existing defensive strategies, and finally explore future trends. Additionally, the survey incorporates diverse case studies to facilitate a more accessible understanding. By highlighting these critical security and privacy issues, the survey seeks to stimulate future research towards enhancing the security and privacy of LLM agents, thereby increasing their reliability and trustworthiness in future applications.
Motion Manifold Flow Primitives for Task-Conditioned Trajectory Generation under Complex Task-Motion Dependencies
Venue: arXiv cs.RO 2025
Year: 2025

Effective movement primitives should be capable of encoding and generating a rich repertoire of trajectories -- typically collected from human demonstrations -- conditioned on task-defining parameters such as vision or language inputs. While recent methods based on the motion manifold hypothesis, which assumes that a set of trajectories lies on a lower-dimensional nonlinear subspace, address challenges such as limited dataset size and the high dimensionality of trajectory data, they often struggle to capture complex task-motion dependencies, i.e., when motion distributions shift drastically with task variations. To address this, we introduce Motion Manifold Flow Primitives (MMFP), a framework that decouples the training of the motion manifold from task-conditioned distributions. Specifically, we employ flow matching models, state-of-the-art conditional deep generative models, to learn task-conditioned distributions in the latent coordinate space of the learned motion manifold. Experiments are conducted on language-guided trajectory generation tasks, where many-to-many text-motion correspondences introduce complex task-motion dependencies, highlighting MMFP's superiority over existing methods.
VolDoGer: LLM-assisted Datasets for Domain Generalization in Vision-Language Tasks
Venue: arXiv cs.CL 2025
Year: 2025

Domain generalizability is a crucial aspect of a deep learning model since it determines the capability of the model to perform well on data from unseen domains. However, research on the domain generalizability of deep learning models for vision-language tasks remains limited, primarily because of the lack of required datasets. To address these challenges, we propose VolDoGer: Vision-Language Dataset for Domain Generalization, a dedicated dataset designed for domain generalization that addresses three vision-language tasks: image captioning, visual question answering, and visual entailment. We constructed VolDoGer by extending LLM-based data annotation techniques to vision-language tasks, thereby alleviating the burden of recruiting human annotators. We evaluated the domain generalizability of various models, ranging from fine-tuned models to a recent multimodal large language model, through VolDoGer.
Rosetta Statements: Simplifying FAIR Knowledge Graph Construction with a User-Centered Approach
Venue: arXiv cs.DB 2025
Year: 2025

Machines need data and metadata to be machine-actionable and FAIR (findable, accessible, interoperable, reusable) to manage increasing data volumes. Knowledge graphs and ontologies are key to this, but their use is hampered by high access barriers due to required prior knowledge in semantics and data modelling. The Rosetta Statement approach proposes modeling English natural language statements instead of a mind-independent reality. We propose a metamodel for creating semantic schema patterns for simple statement types. The approach supports versioning of statements and provides a detailed editing history. Each Rosetta Statement pattern has a dynamic label for displaying statements as natural language sentences. Implemented in the Open Research Knowledge Graph (ORKG) as a use case, this approach allows domain experts to define data schema patterns without needing semantic knowledge. Future plans include combining Rosetta Statements with semantic units to organize ORKG into meaningful subgraphs, improving usability. A search interface for querying statements without needing SPARQL or Cypher knowledge is also planned, along with tools for data entry and display using Large Language Models. The Rosetta Statement metamodel supports a three-step knowledge graph construction procedure. Domain experts can model semantic content without support from ontology engineers by using Wikidata, lowering entry barriers and increasing cognitive interoperability. The second level involves mapping Wikidata terms to established ontologies, and the third step developing semantic graph patterns for reasoning, requiring collaboration with ontology engineers.
Hierarchically Disentangled Recurrent Network for Factorizing System Dynamics of Multi-scale Systems: An application on Hydrological Systems
Venue: arXiv cs.LG 2025
Year: 2025

We present a framework for modeling multi-scale processes, and study its performance in the context of streamflow forecasting in hydrology. Specifically, we propose a novel hierarchical recurrent neural architecture that factorizes the system dynamics at multiple temporal scales and captures their interactions. This framework consists of an inverse and a forward model. The inverse model is used to empirically resolve the system's temporal modes from data (physical model simulations, observed data, or a combination of them from the past), and these states are then used in the forward model to predict streamflow. Experiments on several catchments from the National Weather Service North Central River Forecast Center show that FHNN outperforms standard baselines, including physics-based models and transformer-based approaches. The model demonstrates particular effectiveness in catchments with low runoff ratios and colder climates. We further validate FHNN on the CAMELS (Catchment Attributes and MEteorology for Large-sample Studies), which is a widely used continental-scale hydrology benchmark dataset, confirming consistent performance improvements for 1-7 day streamflow forecasts across diverse hydrological conditions. Additionally, we show that FHNN can maintain accuracy even with limited training data through effective pre-training strategies and training global models.
rLLM: Relational Table Learning with LLMs
Venue: arXiv cs.AI 2025
Year: 2025

We introduce rLLM (relationLLM), a PyTorch library designed for Relational Table Learning (RTL) with Large Language Models (LLMs). The core idea is to decompose state-of-the-art Graph Neural Networks, LLMs, and Table Neural Networks into standardized modules, to enable the fast construction of novel RTL-type models in a simple "combine, align, and co-train" manner. To illustrate the usage of rLLM, we introduce a simple RTL method named \textbf{BRIDGE}. Additionally, we present three novel relational tabular datasets (TML1M, TLF2K, and TACM12K) by enhancing classic datasets. We hope rLLM can serve as a useful and easy-to-use development framework for RTL-related tasks. Our code is available at: https://github.com/rllm-project/rllm.
Machine Learning for Predicting Chaotic Systems
Venue: arXiv cs.LG 2025
Year: 2025

Predicting chaotic dynamical systems is critical in many scientific fields, such as weather forecasting, but challenging due to the characteristic sensitive dependence on initial conditions. Traditional modeling approaches require extensive domain knowledge, often leading to a shift towards data-driven methods using machine learning. However, existing research provides inconclusive results on which machine learning methods are best suited for predicting chaotic systems. In this paper, we compare different lightweight and heavyweight machine learning architectures using extensive existing benchmark databases, as well as a newly introduced database that allows for uncertainty quantification in the benchmark results. In addition to state-of-the-art methods from the literature, we also present new advantageous variants of established methods. Hyperparameter tuning is adjusted based on computational cost, with more tuning allocated to less costly methods. Furthermore, we introduce the cumulative maximum error, a novel metric that combines desirable properties of traditional metrics and is tailored for chaotic systems. Our results show that well-tuned simple methods, as well as untuned baseline methods, often outperform state-of-the-art deep learning models, but their performance can vary significantly with different experimental setups. These findings highlight the importance of aligning prediction methods with data characteristics and caution against the indiscriminate use of overly complex models.
Radiance Fields for Robotic Teleoperation
Venue: arXiv cs.RO 2025
Year: 2025

Radiance field methods such as Neural Radiance Fields (NeRFs) or 3D Gaussian Splatting (3DGS), have revolutionized graphics and novel view synthesis. Their ability to synthesize new viewpoints with photo-realistic quality, as well as capture complex volumetric and specular scenes, makes them an ideal visualization for robotic teleoperation setups. Direct camera teleoperation provides high-fidelity operation at the cost of maneuverability, while reconstruction-based approaches offer controllable scenes with lower fidelity. With this in mind, we propose replacing the traditional reconstruction-visualization components of the robotic teleoperation pipeline with online Radiance Fields, offering highly maneuverable scenes with photorealistic quality. As such, there are three main contributions to state of the art: (1) online training of Radiance Fields using live data from multiple cameras, (2) support for a variety of radiance methods including NeRF and 3DGS, (3) visualization suite for these methods including a virtual reality scene. To enable seamless integration with existing setups, these components were tested with multiple robots in multiple configurations and were displayed using traditional tools as well as the VR headset. The results across methods and robots were compared quantitatively to a baseline of mesh reconstruction, and a user study was conducted to compare the different visualization methods. For videos and code, check out https://rffr.leggedrobotics.com/works/teleoperation/.
NeuSemSlice: Towards Effective DNN Model Maintenance via Neuron-level Semantic Slicing
Venue: arXiv cs.LG 2025
Year: 2025

Deep Neural networks (DNNs), extensively applied across diverse disciplines, are characterized by their integrated and monolithic architectures, setting them apart from conventional software systems. This architectural difference introduces particular challenges to maintenance tasks, such as model restructure (e.g., model compression), re-adaptation (e.g., fitting new samples), and incremental development (e.g., continual knowledge accumulation). Prior research addresses these challenges by identifying task-critical neuron layers, and dividing neural networks into semantically-similar sequential modules. However, such layer-level approaches fail to precisely identify and manipulate neuron-level semantic components, restricting their applicability to finer-grained model maintenance tasks. In this work, we implement NeuSemSlice, a novel framework that introduces the semantic slicing technique to effectively identify critical neuron-level semantic components in DNN models for semantic-aware model maintenance tasks. Specifically, semantic slicing identifies, categorizes and merges critical neurons across different categories and layers according to their semantic similarity, enabling their flexibility and effectiveness in the subsequent tasks. For semantic-aware model maintenance tasks, we provide a series of novel strategies based on semantic slicing to enhance NeuSemSlice. They include semantic components (i.e., critical neurons) preservation for model restructure, critical neuron tuning for model re-adaptation, and non-critical neuron training for model incremental development. A thorough evaluation has demonstrated that NeuSemSlice significantly outperforms baselines in all three tasks.